Defense Secretary Robert Gates predicted Friday during a visit to San Diego that the region’s sizable military and defense community could expect a smaller Marine Corps and other deep changes as the Pentagon embarks on a major reorganization.

Gates hopes to cut $100 billion over the next five years in overhead and nonessential weapons programs to channel more resources to war fighters.

It is difficult to determine the impact on San Diego County before the Navy Department sets its priorities, Gates said, speaking at Marine Corps Recruit Depot San Diego. But based on his comments in recent days, potential crosscurrents facing the area include:

• A smaller force of Marines stationed at Camp Pendleton and supporting bases.

• More money for shipbuilding and other critical equipment.

• A 10 percent cut in overall defense contracting.

• More efficient command staffs, including elimination of some general and admiral positions.

The Pentagon’s spending in San Diego County is significant. In 2008, the most recent year available, the overall impact amounted to $26.5 billion in output and 328,000 jobs, according to a study by the San Diego Military Advisory Council.

During his two-day visit to San Diego, Gates said “there is a future for the Marine Corps, but it isn’t as a second land Army. And that is what the new commandant is going to have to address.

“The future mission has to be true to the maritime missions and expertise of the Corps,” Gates said Friday. “It has to be expeditionary. I agree with (Marine commandant, Gen. James T.) Conway that it needs to be lighter.”

A sailor asked Gates during a visit Thursday to the destroyer Higgins at San Diego Naval Base how the streamlining would affect his shipmates.

If the Pentagon budget works out the way he intends, “they’ll get the money,” Gates said, though he added that the number of Navy personnel, now at about 330,000, is unlikely to expand. “I want it to go into our force structure. I want it to go into modernization and investments in future capabilities.”

He said he is especially concerned about making sure the Marines and sailors he met in San Diego have the tools they need to do their jobs, whether it’s training troops or fixing engines.

“The whole purpose is really to slim down on overhead and bureaucracy and large staffs, and try and convert that from tail to tooth for the long run,” Gates said.

Gates announced plans Monday to shutter a major command based in Virginia that employs about 5,000 people. On Thursday, Gates said he ordered a Force Structure Review for the Marine Corps, which tasked commanders with defining what makes the Marines unique from the Army.

To cope with the strain of years of ground combat in Afghanistan and Iraq, the Corps grew from 175,000 to 202,000 Marines. It will likely shrink again as troops draw down in Afghanistan, Gates and other military leaders said, but by how much remains in doubt.

Gates has also questioned whether large-scale amphibious landings along the lines of the Korean War invasion of Inchon in 1950 are still feasible, striking at one of the unique capabilities of the Marine “soldiers of the sea.”

But many defense analysts say that, even in the age of long-range missiles, the flexibility of deploying Marine forces from Navy ships for humanitarian, training and combat missions remains invaluable.

The problem is that it is expensive, said Dakota Wood, a retired Marine and senior fellow at the Center for Strategic and Budgetary Assessments.

“It is no small feat to build a sizable amphibious ship and to field the type of force that you would put inside that ship, with the skill set needed to organize and execute an amphibious operation,” he said. “It’s a fairly complex military operation. It takes a lot of time and expertise to do it well.”

Gates said he has asked all of the service chiefs to identify priorities for how they want to reinvest the funding obtained from more efficient oversight.

“I don’t know what the impact of some of the decisions the Navy will make will have on San Diego,” Gates said Friday. “But I can tell you if it involves ships, readiness, force structure, weapons, future capabilities — those are all areas I would like to see get more money.

“On the other hand, if you have an overstaffed headquarters, you might have a problem,” he said.

During his visit to the recruit depot, Gates served as the parade reviewing officer for a company of 196 new Marines. Then he watched recruits tumble and pummel their way through combat training. The young men, sweat trickling down their dusty faces, paused to catch their breaths and pose for pictures with Gates.

During his stay in San Diego, Gates also visited San Diego Naval Medical Center at Balboa Park and a class of Navy SEAL recruits in Coronado.

“It takes uncommon patriotism to join the military in a time of war,” Gates told the Marines.

“For my part, I will do all I can to see that you have everything you need to accomplish your mission and come home safely, because I feel a deep personal responsibility for every one of you, as if you were my own sons.”